It's a busy time in our attempts to study our species' pre-modern history. Just two weeks ago, researchers reported the sequence of the oldest bones to yield human DNA. Now, the same research group is back with an entire genome, obtained from a bone found in Siberia's Denisova cave. This genome comes from a Neanderthal, but all the data reveals a lot about all the interconnections among the pre-modern human groups that were wandering around Eurasia tens of thousands of years ago. The analysis came with a tantalizing hint that one of those groups had interbred with a species separated from modern humans by over a million years—perhaps Homo erectus.

The Denisova cave is famous for having yielded the bones that helped us identify the Denisovans, a group of archaic humans that inhabited Asia at the same time as the Neanderthals. Although we haven't found enough bones to know much about what the Denisovans looked like, DNA analysis has revealed that they are most closely related to Neanderthals and that they interbred with modern humans that went on to populate East Asia, the Americas, and the Pacific.

The new results spring from a toe bone found in the same cave, this one from a layer that is estimated to be tens of thousands of years earlier. DNA sequencing revealed the bone to be from a Neanderthal, a different group of pre-modern humans that is most closely related to the Denisovans. The DNA was in excellent condition and had a minimal (about one percent) contamination with sequences from modern humans. The team generated a high-quality genome using samples from this bone.

The sequence that resulted tells us a lot about Neanderthals. For one, it shows that other populations we've obtained DNA from (samples found in the Caucasus and Croatia) were closely related but distinct, indicating that the Neanderthals were already well established by the time this individual died. Those populations were apparently quite small, however, since there's not a lot of genetic diversity among them. In the case of the specific individual in the Denisovan cave, the lack of diversity was quite severe. Rather than carrying two distinct sets of chromosomes, large stretches of the two chromosomes were identical, indicating that they were inherited from a single individual in the recent past.

The extent of this identity suggests that the parents of this individual were half-siblings, although other combinations (uncle-niece, aunt-nephew) would also produce a similar pattern.

But the more significant results come from what this new sequence tells us about the other groups of humans present at the time, including modern humans. To begin with, it confirms the rough timing of the split between the ancestors of modern humans and the ancestors of Neanderthals and Denisovans, which took place about 550,000-600,000 years ago. The Neanderthals and Denisovans became a distinct population about 400,000 years ago.

The sequence also provides a clearer estimate of the amount of Neanderthal DNA that shows up in modern human populations: 1.5 to 2.1 percent. And it confirms that it got there via interbreeding, since the Neanderthal sequence looks most similar to the sample obtained from the Caucasus remains. Had it been inherited through a structured ancestral population in Africa, it should look like it was equally distant from all three of the Neanderthal genomes. The other thing that's apparent is that modern Asian and American populations have a bit more Neanderthal DNA than others, suggesting that a low amount of interbreeding continued as our ancestors moved east.

Our ancestors weren't the only ones who couldn't resist getting a piece of the Neanderthals. At least a half percent of the Denisovan genome also came from them as well.

But perhaps the most unexpected finding comes from a comparison with the Denisovan genome. Modern humans in Africa never overlapped geographically with Neanderthals or Denisovans and thus contain none of their DNA. Therefore, any shared DNA they have should be inherited from a common ancestor, and the African's should be equally distant from the Neanderthals and Denisovans. Yet they're not. The Denisovans have some sequences that are much more distant than you'd expect.

After considering and rejecting a couple of alternative explanations for this, the paper settles on a rather radical explanation: Denisovans themselves interbred with a population that had been separated from their common ancestor with modern humans for about a million years. This, as the authors note, suggests that the DNA's source was Homo erectus. In fact, they suggest that the Denisovan's entire mitochondrial genome might have come from this interbreeding event, since it's much more distant from the Neanderthals' than the rest of the genome is.

Of course, that explanation is even harder to square with the findings from the ancient bones in Spain, which had a similar sequence but came from skeletons that looked somewhat like Neanderthals. Unless, of course, the Spanish population also interbred with Homo erectus (or whatever this is) at some point.

In any case, the results add yet another layer onto the increasingly complicated Out-of-Africa model of the origin of modern humans. We still arose in Africa and migrated out into Eurasia. But once we got there, we interbred with a previous wave of African expatriates and incorporated a small bit of their genetic legacy into our own. And one part of that previous wave may have even incorporated a tiny piece of a species that hadn't seen Africa for a very long time.

65 Reader Comments

Whenever I see a story like this I think "Ice Man." The guy from the 90's that they found trapped in the ice and everybody came out of the woodwork to declare that he was the missing link only to find out later that he still had a living grandson...

I hope you aren't referring to Ötzi, the 5300 year old mummy, who most certainly does not have a living grandson.

The one and the same. I remember what I read about him back when the story disappeared from the news and not what everybody claims he is now. He got trapped behind a rock during an avalanche and now he's a mummy?

When the body was first discovered, it was assumed to be a mountaineer who died within the previous few years. It wasn't until they dug it out of the ice that they realized it was much older. It was never considered a "missing link" in the evolutionary sense, being a fully modern human from only a few thousand years ago (much younger than the Neandertals and Denisovans being discussed in the article). No living grandchildren or great-grandchildren (for what are hopefully obvious reasons), but it wouldn't be surprising if some people in that area were his descendents (or at least descended from the same clan). The body and the belongings found with it have huge archaeological value, offering insights into what life was like for people in that area at that time.

The latest analysis of the remains suggests he was a victim of murder or some kind of battle; he had an arrowhead buried in his left shoulder and showed signs of head trauma, along with other peri-mortem injuries. It isn't clear whether he was killed near where he was found, or whether he was carried there from a lower altitude.

Further recent analyst of his stomach, which apparently was hard to find at first as it had migrated high up into his chest cavity, and intestines suggest (from pollen) that he had been high in the mountains, perhaps hunting or looking for copper, then came down to the lowlands, had a fairly large meal (of cooked lamb I think), before returning to the mountains, perhaps while being pursued, after being recently wounded in a vicious attack. All in all A pretty dramatic end.

Speciation is fuzzy because it's not really a thing: it's a category, and therefore fundamentally "artificial". Its purpose is to assist in organizing information, but it is not a discoverable truth unto itself.

I confess, I've always felt that "not being able to interbreed" ought to be the line for species versus sub-species: that seems like a useful distinction to be able to see taxonomically. Yet one can see why there would be resistance: it would cause a huge amount of reclassification (Donkeys, horses and zebras? Same species. Lions and tigers? Same species. Dogs, wolves, coyotes, etc. etc. etc.? Same species. Humans and sheep? Exhaustively demonstrated to not be the same species.)

You could theoretically tighten that by stipulating that members of the same species must be able to produce fertile offspring. Mules, Zorses, Wolphins, Ligers, and Tigons -- I'm not sure any of them are fertile. If they *can* breed, I'm fairly certain the pairings are limited.

Speciation is fuzzy because it's not really a thing: it's a category, and therefore fundamentally "artificial". Its purpose is to assist in organizing information, but it is not a discoverable truth unto itself.

I confess, I've always felt that "not being able to interbreed" ought to be the line for species versus sub-species: that seems like a useful distinction to be able to see taxonomically. Yet one can see why there would be resistance: it would cause a huge amount of reclassification (Donkeys, horses and zebras? Same species. Lions and tigers? Same species. Dogs, wolves, coyotes, etc. etc. etc.? Same species. Humans and sheep? Exhaustively demonstrated to not be the same species.)

You could theoretically tighten that by stipulating that members of the same species must be able to produce fertile offspring. Mules, Zorses, Wolphins, Ligers, and Tigons -- I'm not sure any of them are fertile. If they *can* breed, I'm fairly certain the pairings are limited.

What about ranges where fertility can happen between near intermediates but not members of either end?

Also, there's a TON of interbred ceteacean variants, some successful and swimming with their pods, some not...

Of course, dolphins will also stick their pensu in anything that'll cooperate ...

I confess to not having read the original article, not being a "Nature" subscriber, but I was most interested in this statement, "The sequence also provides a clearer estimate of the amount of Neanderthal DNA that shows up in modern human populations: 1.5 to 2.1 percent." from your article.

Are you able to elaborate at all on how this was derived and whether it applies to all Modern populations that show Neanderthal DNA? I ask because it's a significant departure and refiguring (as far as I know) from previous estimates. A bit of a game changer. Your thoughts are appreciated.

Also nice to see another confirmation of multiple, if limited, interbreeding events.

But, what is the difference between the life that is in a cell, a chimpanzee, a neardenthal or a modern homo sapiens? Do not come and vanishes in the same way, in one breath alone? Isn’t life a single indivisible movement, an information flow that builds up and changes from a common ancestor? So, is the species concept only a weak convention that will dissapear with time too, an ephimeral spark? Or perhaps is there a unique quality in the tree of life, a qualitative leap detached from all evolutionary processes and unrelated to the rest of life? Is it the same leap that the human language makes when differentiating between life and the rest of the universe? Also between human beings and the rest of animals, food and eaters, health and disease, between life and death itself? Along these lines, a book recommendation, a preview in http://goo.gl/rfVqw6 Just another mind leisure suggestion, far away from dogmas or axioms.

Not sure what you are getting at but "species" is definitely a human brain invention and does not reflect any real delineation in nature. Humans love to categorize, "pigeonhole" if you will.

The extent of this identity suggests that the parents of this individual were step siblings....

Shouldn't this be "half-siblings," meaning they share one genetic parent? Step siblings aren't genetically related; a parent of one married a parent of the other after the children were born.

It might shed some light on distinctions between modern humans and Neaderthals. In humans, doing your half-sister is taboo across pretty much all cultures, which might mean that humans instinctively seek less-related mates. Neanderthals might not have shared that characteristic.

But, what is the difference between the life that is in a cell, a chimpanzee, a neardenthal or a modern homo sapiens? Do not come and vanishes in the same way, in one breath alone? Isn’t life a single indivisible movement, an information flow that builds up and changes from a common ancestor? So, is the species concept only a weak convention that will dissapear with time too, an ephimeral spark? Or perhaps is there a unique quality in the tree of life, a qualitative leap detached from all evolutionary processes and unrelated to the rest of life? Is it the same leap that the human language makes when differentiating between life and the rest of the universe? Also between human beings and the rest of animals, food and eaters, health and disease, between life and death itself? Along these lines, a book recommendation, a preview in http://goo.gl/rfVqw6 Just another mind leisure suggestion, far away from dogmas or axioms.

Not sure what you are getting at but "species" is definitely a human brain invention and does not reflect any real delineation in nature. Humans love to categorize, "pigeonhole" if you will.

It does have a basis. It's just that with closely related species, the lines aren't that bright.

The extent of this identity suggests that the parents of this individual were step siblings....

Shouldn't this be "half-siblings," meaning they share one genetic parent? Step siblings aren't genetically related; a parent of one married a parent of the other after the children were born.

It might shed some light on distinctions between modern humans and Neaderthals. In humans, doing your half-sister is taboo across pretty much all cultures, which might mean that humans instinctively seek less-related mates. Neanderthals might not have shared that characteristic.

Regardless of taboo, interbreeding happens. The more isolated a small population is, the more it happens. If you share a cave with your half-sister, a female homo erectus, and your trusty Coopworth sheep and there aren't any sexy Neanderthals around, interbreeding becomes a very likely event. The sheep won't get pregnant, though.

Speciation is fuzzy because it's not really a thing: it's a category, and therefore fundamentally "artificial". Its purpose is to assist in organizing information, but it is not a discoverable truth unto itself.

I confess, I've always felt that "not being able to interbreed" ought to be the line for species versus sub-species: that seems like a useful distinction to be able to see taxonomically. Yet one can see why there would be resistance: it would cause a huge amount of reclassification (Donkeys, horses and zebras? Same species. Lions and tigers? Same species. Dogs, wolves, coyotes, etc. etc. etc.? Same species. Humans and sheep? Exhaustively demonstrated to not be the same species.)

How do you distinguish non-sexual reproduction of species or get around ring species?

Speciation is fuzzy because it's not really a thing: it's a category, and therefore fundamentally "artificial". Its purpose is to assist in organizing information, but it is not a discoverable truth unto itself.

I confess, I've always felt that "not being able to interbreed" ought to be the line for species versus sub-species: that seems like a useful distinction to be able to see taxonomically. Yet one can see why there would be resistance: it would cause a huge amount of reclassification (Donkeys, horses and zebras? Same species. Lions and tigers? Same species. Dogs, wolves, coyotes, etc. etc. etc.? Same species. Humans and sheep? Exhaustively demonstrated to not be the same species.)

How do you distinguish non-sexual reproduction of species or get around ring species?

Messily? .. As Gawain wrote above speciation is a classification system not an actual thing.

Ring species are classically shown as examples if speciation in progress, a transitional state that might eventually lead to fully different species arising, or not. While the ends of the ring may not be able to interbreed each neighbouring link still can. It may be the early hominid groups from erectus - Neanderthal - to us were a ring like species group. Not that there any actual evidence for this but maybe We might not have been able to sucessfully interbreed with those hot erectus chicks down by the mud flats but billy our half neanderthal cousin could get it on. In the case of asexual reproduction, which occasionally happens with larger multicellular animals ( wasn't there recently a shark in a aquarium that did so? .. Maybe it was even a croc? Maybe even some of those virgin human births in our myths, but if so why wasn't jesus a girl?.. ) but mostly is common in single cell organisms and it tends to change thing quite a bit, but on the other hand when asexual reproduction happens you tend to get two organisms with nearly identical genetics, ... So are they really two organisms? Or two incidents of the same organism? So even if they will never interbreed they are all directly related. Things get really confusing when these same organisms exchange genetic material with other organisms which aren't even genetically related thru descent, this is especially tricky with bacteria and the like who do so often but also is very common in plants especially much of what we eat, ... So really .. What do you call that? ... So seriously ... Using species as a way to classify organism like using hair style to classify musicians works fairly well most of the time, ... But it dosen't in it self actually have any have any definitive truth, .. Its just a conviniant way of trying to make some sense of what going on.

I found your liberal usage of the term 'human' to be inaccurate, such as:

Quote:

DNA sequencing revealed the bone to be from a Neanderthal, a different group of pre-modern humans that is most closely related to the Denisovans.

[

Homo Neanderthalensis (Neaderthal) is a different species than Homo Sapiens (Human). The term human should only be applied to refer to Homo Sapiens and it's sub-species, Cro-Magnon, correctly referred to as European Early Modern Humans (EEMH), and Homo Sapiens Sapiens (Modern Humans).

Also, i believe the species Homo Habilis had two descendant species: Homo Erectus, which migrated into Asia, and Homo Georgicus, which migrated into Europe. So, Homo Georgicus should be used in reference to this article rather than Homo Erectus.

Speciation is fuzzy because it's not really a thing: it's a category, and therefore fundamentally "artificial". Its purpose is to assist in organizing information, but it is not a discoverable truth unto itself.

I confess, I've always felt that "not being able to interbreed" ought to be the line for species versus sub-species: that seems like a useful distinction to be able to see taxonomically. Yet one can see why there would be resistance: it would cause a huge amount of reclassification (Donkeys, horses and zebras? Same species. Lions and tigers? Same species. Dogs, wolves, coyotes, etc. etc. etc.? Same species. Humans and sheep? Exhaustively demonstrated to not be the same species.)

How do you distinguish non-sexual reproduction of species or get around ring species?

Messily? .. As Gawain wrote above speciation is a classification system not an actual thing.

Ring species are classically shown as examples if speciation in progress, a transitional state that might eventually lead to fully different species arising, or not. While the ends of the ring may not be able to interbreed each neighbouring link still can. It may be the early hominid groups from erectus - Neanderthal - to us were a ring like species group. Not that there any actual evidence for this but maybe We might not have been able to sucessfully interbreed with those hot erectus chicks down by the mud flats but billy our half neanderthal cousin could get it on. In the case of asexual reproduction, which occasionally happens with larger multicellular animals ( wasn't there recently a shark in a aquarium that did so? .. Maybe it was even a croc? Maybe even some of those virgin human births in our myths, but if so why wasn't jesus a girl?.. ) but mostly is common in single cell organisms and it tends to change thing quite a bit, but on the other hand when asexual reproduction happens you tend to get two organisms with nearly identical genetics, ... So are they really two organisms? Or two incidents of the same organism? So even if they will never interbreed they are all directly related. Things get really confusing when these same organisms exchange genetic material with other organisms which aren't even genetically related thru descent, this is especially tricky with bacteria and the like who do so often but also is very common in plants especially much of what we eat, ... So really .. What do you call that? ... So seriously ... Using species as a way to classify organism like using hair style to classify musicians works fairly well most of the time, ... But it doesn't in it self actually have any have any definitive truth, .. Its just a conviniant way of trying to make some sense of what going on.

Gawain Lavers also said:

Quote:

I confess, I've always felt that "not being able to interbreed" ought to be the line for species versus sub-species: that seems like a useful distinction to be able to see taxonomically.

to which I should have directed my question more precisely. But your informative post explaining why I was questioning this statement didn't work out is appreciated. And even as I write this I wonder if it was something Gawain Lavers probably knew, given what you point out he responded with earlier. I'll acknowledge I focused on the wrong point.

I confess to not having read the original article, not being a "Nature" subscriber, but I was most interested in this statement, "The sequence also provides a clearer estimate of the amount of Neanderthal DNA that shows up in modern human populations: 1.5 to 2.1 percent." from your article.

Are you able to elaborate at all on how this was derived and whether it applies to all Modern populations that show Neanderthal DNA? I ask because it's a significant departure and refiguring (as far as I know) from previous estimates. A bit of a game changer. Your thoughts are appreciated.

Also nice to see another confirmation of multiple, if limited, interbreeding events.

Homo Neanderthalensis (Neaderthal) is a different species than Homo Sapiens (Human). The term human should only be applied to refer to Homo Sapiens and it's sub-species, Cro-Magnon, correctly referred to as European Early Modern Humans (EEMH), and Homo Sapiens Sapiens (Modern Humans).

That's your definition. Human could be a term applied to any organism of the genus Homo, including Homo erectus.

Speciation is such a fuzzy, hard to define thing anyway.

Quite a few species are regional specific variants of a broader group, and easily capable of interbreeding, should opportunity exist. Others exist in a gradient with regional epitomes with a broad range in the middle.

If you look at humans, the various subgroups are conventionally considered regional subgroups, but using some of the other classification methodology, could be different but related species altogether.

For instance, prior to people sailing regularly across the Atlantic ocean, New World populations might have been considered a separate species from Old World humans by hypothetical aliens visiting from another world because: no evidence of gene exchange for thousands of years.

Maybe we should have some sort of standard for how long populations need to be separated or a degree of genetic divergence before we slap a species monicker on a group of organisms.

The extent of this identity suggests that the parents of this individual were step siblings....

Shouldn't this be "half-siblings," meaning they share one genetic parent? Step siblings aren't genetically related; a parent of one married a parent of the other after the children were born.

It might shed some light on distinctions between modern humans and Neaderthals. In humans, doing your half-sister is taboo across pretty much all cultures, which might mean that humans instinctively seek less-related mates. Neanderthals might not have shared that characteristic.

Regardless of taboo, interbreeding happens. The more isolated a small population is, the more it happens. If you share a cave with your half-sister, a female homo erectus, and your trusty Coopworth sheep and there aren't any sexy Neanderthals around, interbreeding becomes a very likely event. The sheep won't get pregnant, though.

In modern humans, it's relatively rare. With the very small number of Neanderthals sequenced, it seems funny to observe evidence of it so quickly. It shouldn't be presumed that the people who happened to leave their bones in that cave were isolated. They were part of a larger population similar to paleolithic and neolithic modern humans, who mostly situated near significant food sources or moved around following herds and such.

Sure, we find their bones in caves because (1) that's where bones are most likely to be preserved and (2) when people are near caves, they use often use them.

Maybe we should have some sort of standard for how long populations need to be separated or a degree of genetic divergence before we slap a species monicker on a group of organisms.

Nah, it's a perfectly fine word indicating a fairly clear concept. However, it's very loaded with implicit assumptions that get squicky when it comes to humans. "Oh, I'm an X, those people are a Y (different) species, it's okay to do blahblah to them as they're not us" is one of the hazards, especially if you start classifying modern humans and human ancestors.

Yeah, the fact that anyone is suprised that we interbred with Neanderthals at some point shocks me. People "lay" with farm animals, why not something that looks mostly like us? I mean, heck, furrys and plushies are a thing!

It doesn't take much more than someone to have an uncle cletus in their caveman tribe to get some of those genes going.

Although we have every reason to believe that archaic humans saw each other as humans, they were also more different from each other than today's "races." Maybe some kind of Uncanny Valley effect kept the number of cross-breeding events to a minimum.

Yeah, the fact that anyone is suprised that we interbred with Neanderthals at some point shocks me. People "lay" with farm animals, why not something that looks mostly like us? I mean, heck, furrys and plushies are a thing!

It doesn't take much more than someone to have an uncle cletus in their caveman tribe to get some of those genes going.

Although we have every reason to believe that archaic humans saw each other as humans, they were also more different from each other than today's "races." Maybe some kind of Uncanny Valley effect kept the number of cross-breeding events to a minimum.

I think it is more interesting, now, that it appears that at least 4 Archaic Human species, or sub-species, were capable of interbreeding, with viable offspring.

Homo Neanderthalensis (Neaderthal) is a different species than Homo Sapiens (Human). The term human should only be applied to refer to Homo Sapiens and it's sub-species, Cro-Magnon, correctly referred to as European Early Modern Humans (EEMH), and Homo Sapiens Sapiens (Modern Humans).

That's your definition. Human could be a term applied to any organism of the genus Homo, including Homo erectus.

Speciation is such a fuzzy, hard to define thing anyway.

Quite a few species are regional specific variants of a broader group, and easily capable of interbreeding, should opportunity exist. Others exist in a gradient with regional epitomes with a broad range in the middle.

If you look at humans, the various subgroups are conventionally considered regional subgroups, but using some of the other classification methodology, could be different but related species altogether.

For instance, prior to people sailing regularly across the Atlantic ocean, New World populations might have been considered a separate species from Old World humans by hypothetical aliens visiting from another world because: no evidence of gene exchange for thousands of years.

Maybe we should have some sort of standard for how long populations need to be separated or a degree of genetic divergence before we slap a species monicker on a group of organisms.

There may never had been a period where the new world and old world did not have some low level of genetic exchange, at least not on the time scale of speciation. Besides the fairly common mass migrations there's some evidence that intermittent trade existed between most major human population groups, and with humans being what they are likely some level of interbreeding, perhaps far back into prehistory, and then as now allot of that trade was drugs ... Sounds pretty far fetched I know, ... But extensive test on Egyptian mummies have shown them to have been users of coke and tobacco ... Which is kinda mind blowing.

Speciation is fuzzy because it's not really a thing: it's a category, and therefore fundamentally "artificial". Its purpose is to assist in organizing information, but it is not a discoverable truth unto itself.

I confess, I've always felt that "not being able to interbreed" ought to be the line for species versus sub-species: that seems like a useful distinction to be able to see taxonomically. Yet one can see why there would be resistance: it would cause a huge amount of reclassification (Donkeys, horses and zebras? Same species. Lions and tigers? Same species. Dogs, wolves, coyotes, etc. etc. etc.? Same species. Humans and sheep? Exhaustively demonstrated to not be the same species.)

You could theoretically tighten that by stipulating that members of the same species must be able to produce fertile offspring. Mules, Zorses, Wolphins, Ligers, and Tigons -- I'm not sure any of them are fertile. If they *can* breed, I'm fairly certain the pairings are limited.

You're overlooking several exotic housecat breeds, which are actually hybrids of domesticated cats and other species (chausie, bengal, savannah, etc.), and seem to breed just fine.